Luisa Di Paola

Campus Bio-Medico University | unicampus ·  Faculty of Engineering

In the past two decades, advancements in thermochemical technologies have improved biomass gasification for distributed power generation, enhancing efficiency, scalability, and emission control. This study aims to optimize syngas production from biomass gasification by comparing two computational models: a quasi-equilibrium thermodynamic model impl...

This paper presents a quasi-analytical method that allows the derivation of a rigorous series-form representation for the mutual inductance of two co-axial coil antennas located above an arbitrarily layered earth structure. Starting from Biot–Savart law, which gives the integral representation for the primary vector potential generated by the sourc...

Fish wastes pose environmental and economic challenges for companies operating in the field. The global fishing industry generates a substantial amount of waste, which has far-reaching consequences. Just to have a glance of the issue on a global scale, according to the Food and Agriculture Organization of the United Nations (FAO), nearly 50 million...

Biomass gasification has obtained great interest over the last few decades as an effective and trustable technology to produce energy and fuels with net-zero carbon emissions. Moreover, using biomass waste as feedstock enables the recycling of organic wastes and contributing to circular economy goals, thus reducing the environmental impacts of wast...

Biomass gasification acquired great interest over the past decades as an effective and trustable technology to produce energy and fuels with net-zero carbon emissions. Moreover, using biomass waste as feedstock enables to recycle organic wastes and to fit the circular economy goals thus reducing the environmental impacts of waste management. Even i...

Tumor necrosis factor receptor-associated factor proteins (TRAFs) are trimeric proteins that play a fundamental role in signaling, acting as intermediaries between the tumor necrosis factor (TNF) receptors and the proteins that transmit the downstream signal. The monomeric subunits of all the TRAF family members share a common tridimensional struct...

The structure of proteins impacts directly on the function they perform. Mutations in the primary sequence can provoke structural changes with consequent modification of functional properties. SARS-CoV-2 proteins have been extensively studied during the pandemic. This wide dataset, related to sequence and structure, has enabled joint sequence-struc...

The structure of proteins impacts directly on the function they perform.Mutations in the primary sequence can provoke structural changes with consequent modification of functional properties. SARS-CoV-2 viral proteins have been extensively studied during the pandemic. Thus, a considerable body of data related to sequence and structure is available,...

Factor VIII belongs to the coagulation cascade and is expressed as a long pre-protein (mature form, 2351 amino acids long). FVIII is deficient or defective in hemophilic A patients, who need to be treated with hemoderivatives or recombinant FVIII substitutes, i.e., biologic drugs. The interaction between FVIII and von Willebrand factor (VWF) influe...

Activation of G-protein-coupled receptors (GPCRs) is mediated by molecular switches throughout the transmembrane region of the receptor. In this work, we continued along the path of a previous computational study wherein energy transport in the β2 Adrenergic Receptor (β2-AR) was examined and allosteric switches were identified in the molecular stru...

Motivation Protein Contact Network (PCN) is a powerful method for analysing the structure and function of proteins, with a specific focus on disclosing the molecular features of allosteric regulation through the discovery of modular substructures. The importance of PCN analysis has been shown in many contexts, such as the analysis of SARS-CoV-2 Spi...

At the center of the SARS-CoV2 infection, the spike protein and its interaction with the human receptor ACE2 play a central role in the molecular machinery of SARS-CoV2 infection of human cells. Vaccine therapies are a valuable barrier to the worst effects of the virus and to its diffusion, but the need of purposed drugs is emerging as a core targe...

ABSTRACT: At the center of the SARS-CoV2 infection, the spike protein and its interaction with the human receptor ACE2 play a central role in the molecular machinery of SARS-CoV2 infection of human cells. Vaccine therapies are a valuable barrier to the worst effects of the virus and to its diffusion, but the need of purposed drugs is emerging as a...

Protein Contact Network (PCN) is an emerging paradigm for modelling protein structure. A common approach to interpreting such data is through network-based analyses. It has been shown that clustering analysis may discover allostery in PCN. Nevertheless Network Embedding has shown good performances in discovering hidden communities and structures in...

TNF Receptor-Associated Factor 2 (TRAF2) is a homo-trimer belonging to the TNF-receptor-associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding, the interaction with other proteins (involved in the TNFR signaling), and the interaction with biological membranes. In this study, we present a computational analysis...

Symmetry is an intrinsic property of homo-oligomers. Amine oxidases are multidomain homodimeric enzymes that contain one catalytic site per subunit, and that share a high homology degree. In this paper, we investigated, by fluorescence spectroscopy measurements, the conformational dynamics and resiliency in solutions of two amine oxidases, one from...

Protein Contact Network (PCN) is a powerful tool for analysing the structure and function of proteins. In particular, PCN has been used for disclosing the molecular features of allosteric regulation through PCN clustering. Such analysis is relevant in many applications, such as the recent study of SARS-CoV-2 Spike Protein. Despite its relevance, me...

TNF Receptor Associated Factor 2 (TRAF2) is a trimeric protein that belongs to the TNF receptor associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding and for its interaction with other proteins involved in the TNFR signaling. The monomer-trimer equilibrium of a C- terminal domain truncated form of TRAF2 (TRAF2...

Structural and biochemical studies of the severe acute respiratory syndrome (SARS)-CoV-2 spike glycoproteins and complexes with highly potent antibodies have revealed multiple conformation-dependent epitopes highlighting conformational plasticity of spike proteins and capacity for eliciting specific binding and broad neutralization responses. In th...

Human aromatase is a member of the cytochrome P450 superfamily, involved in steroid hormones biosynthesis. In particular, it converts androgen into estrogens being therefore responsible for the correct sex steroids balance. Due to its capacity in producing estrogens it has also been considered as a promising target for breast cancer therapy. Two si...

Human aromatase is a member of the cytochrome P450 superfamily, involved in steroid hormones biosynthesis. In particular, it converts androgen into estrogens being therefore responsible for the correct sex steroids balance. Due to its capacity in producing estrogens it has also been considered as a promising target for breast cancer therapy. Two si...

The structural and biochemical studies of the SARS-CoV-2 spike glycoproteins and complexes with highly potent antibodies have revealed multiple conformation-dependent epitopes highlighting the link between conformational plasticity of spike proteins and capacity for eliciting specific binding and broad neutralization responses. In this study, we us...

The rapidly growing body of structural and biochemical studies of the SARS-CoV-2 spike glycoprotein has revealed a variety of distinct functional states with radically different arrangements of the receptor-binding domain, highlighting a remarkable function-driven conformational plasticity and adaptability of the spike proteins. In this study, we e...

In this paper we report a procedure to analyze protein homodimer interfaces.We approached the problem by means of a topological methodology. In particular, we analyzed the subunits interface of about 50 homodimers and we have defined a few parameters that allow to organize these proteins in six different classes. The main characteristics of each cl...

Proteins are located in the twilight zone between chemistry and biology, where a peculiar kind of complexity starts. Proteins are the smallest ‘devices’ showing a sensible adaptation to their environment by the production of appropriate behavior when facing a specific stimulus. This fact qualifies (from the ‘effector’ side) proteins as nanomachines...

This volume explores the basic issues of “allostery” and “network” that are fundamental to studying this field. Chapters in this book look at how the basic “machine-like” proteins, that are similar to “human machines,” need to be organized, architecturally, to relate to different organizational layers. Chapters cover topics such as methodological/c...

The search for new biological sources of commercial value is a major goal for the sustainable management of natural resources. The huge amount of fishery by-catch or processing by-products continuously produced needs to be managed to avoid environmental problems and keep resource sustainability. Fishery by-products can represent an interesting sour...

Growing interest in hypertension—one of the main factors characterizing the cardiometabolic syndrome (CMS)—and anti-hypertensive drugs raised from the emergence of a new coronavirus, SARS-CoV-2, responsible for the COVID19 pandemic. The virus SARS-CoV-2 employs the Angiotensin-converting enzyme 2 (ACE2), a component of the RAAS (Renin- Angiotensin-...

SARS-CoV-2 has caused the largest pandemic of the XXI (COVID-19), threatening the life and economy of all countries in the world. Finding therapies and vaccines to mitigate or even fight this sanitary and health threat is among the most important challenges of biomedical sciences in the century. To build up a long-term strategy to fight not only SA...

The tumor necrosis factor (TNF) superfamily (TNFSF) includes about thirty structurally related receptors (TNFSFRs) and about twenty protein ligands that bind to one or more of these receptors. Receptors of the tumor necrosis factor (TNF) superfamily (TNFSFRs) are pharmacological targets for treatment of inflammatory and autoimmune diseases. Current...

Coronaviruses are a class of virus responsible of the recent outbreak of Human Severe Acute Respiratory Syndrome. The molecular machinery behind the viral entry and thus infectivity is based on the formation of the complex of virus spike protein with the angiotensin-converting enzyme 2 (ACE2). The detection of putative allosteric sites on the viral...

The ELAVL1 (or human antigen R - HuR) RNA binding protein stabilizes the mRNA, with an AU-rich element, of several genes such as growth factors (i.e. VEGF) and inflammatory cytokines (i.e. TNFα). We hereby carried out a virtual screening campaign in order to identify and test novel HuR-mRNA disruptors. Best-scored compounds were tested in an in-vit...

The oligomeric state of TRAF2 (tumor necrosis factor-receptor associated factor 2), a TNF (tumor necrosis factor) receptor-associated factor, is crucial for membrane binding and probably plays a fundamental role in regulating the protein function in vivo. In this study we have combined molecular dynamics with the protein contact network approach to...

The production of biogas requires the development of cheap and effective inline monitoring of 11 systems; specifically, pure biogas for specialized applications (solid oxide fuel cells) needs 12 very low concentrations of volatile organic compounds' contaminants. In this work, we report an application of a system, Bionote, already tested at very lo...

Background: Protein-protein interactions embody the main target of drug discovery due to their vast presence in physiological mechanisms. Hence, targeting protein-protein interfaces is actually the “holy grail” of pharmacology. Much is known about the binding of small molecules to single peptide chains, but much more is still to be discovered about...

An advection–diffusion–reaction transport model for a continuous reactor characterized by a simple geometry is simulated to provide a design guidance for the realization of an optimized experimental prototype consisting of a rectangular channel hosting a scaffold slab that provides an immobilizing support for the cells. A counter‐current carrier fl...

Inferring functional properties of a node from its topological role in the network is of utmost importance in many application fields. In this work, we try to give some hints on this issue focusing on the discovery of empirical topology/function rules located at different degrees of generalization going from a population of heterogeneous biological...

Significance The maintenance of boundaries between neighboring groups of distinct cell types is vital during development of multicellular organisms, as groups of cells with distinct functions must be kept physically separated to guarantee correct control of organ and body growth and function. In the Arabidopsis root, the transition zone is a develo...

The amazing variety of protein functions are often covered by protein complexes, so understanding protein–protein interactions means coming deeply into the functional role of proteins in life. In the last years, the investigation of protein–protein interactions has become central in many fields, spanning from molecular biology to pharmacology. In t...

Diabetic retinopathy (DR) is the most frequent complication of diabetes and one of leading causes of blindness worldwide. Early phases of DR are characterized by retinal pericyte loss mainly related to concurrent inflammatory process. Recently, an important link between P2X7 receptor (P2X7R) and inflammation has been demonstrated indicating this re...

Among the thermal desalination process, the humidification-dehumidification (HDH) is quite energy demanding due to the presence of circulating air (as water carrier from the saline source to the condensation unit) that increases the required interface areas. Nevertheless, this process shows many unique attributes that are pushing a recent revival o...

Although, the recent efforts in the field of sustainable shipping, the energy efficiency is still limited at a half of the fuel calorific value, whereas the spare input energy is discharged in the environment as exhausted gas and jacket water. It is possible to increase the overall engine efficiency virtually up to 80% by introducing a Combined Ran...

The overall topology and interfacial interactions play key roles in understanding structural and functional principles of protein complexes. Elastic Network Model (ENM) and Protein Contact Network (PCN) are two widely used methods for high throughput investigation of structures and interactions within protein complexes. In this work, the comparativ...

Figure S1 (a) shows that R2-Hb demonstrates different intrinsic dynamics with T-HB, and Figure S1 (b) detects that the second ANM mode of T-Hb contribute the most for the conformational change from T-state to R2 state. Figure S1 (c) shows that R2-Hb has similar intrinsic dynamics with R-Hb. Distribution of mean-square fluctuations shown in Figure S...

In the next few years the world demand for liquid fossil fuels for transportation will require finding a reliable and feasible alternative. Bio-oil represents an interesting choice because of the properties of upgraded products, which are good candidates for a drop-in fuel.With this perspective, optimization of bio-oil production necessitates proce...

Key message The application of Protein Contact Networks methodology allowed to highlight a novel response of border region between the two domains to substrate binding. Abstract Glycoside hydrolases (GH) are enzymes that mainly hydrolyze the glycosidic bond between two carbohydrates or a carbohydrate and a non-carbohydrate moiety. These enzymes are...

Produced waters (PW) are the largest waste associated to the production of oil and gas; they contain dissolved salts, oil (dissolved and scattered organic compounds), chemicals and salt intolerant additives to the oil well operations, suspended particles, sand and other compounds, making their treatment very tricky. In this paper, we propose the us...

Microflow reactors provide an ideal environment for the artificial growth of biological tissues, since temperature and concentration of the chemical species can be accurately controlled. In this work, we present an analysis of transport regimes and mechanisms underlying the cell activity in the microenvironment, in terms of reaction rates, product...

Anthrax toxin comprises three different proteins, jointly acting to exert toxic activity: a non-toxic protective agent (PA), toxic edema factor (EF), and lethal factor (LF). Binding of PA to anthrax receptors promotes oligomerization of PA, binding of EF and LF, and then endocytosis of the complex. Homomeric forms of PA, complexes of PA bound to LF...

Anti-angiogenic agents are biological drugs used for treatment of retinal neovascular degenerative diseases. In this study, we aimed at in silico analysis of interaction of vascular endothelial growth factor A (VEGFA), the main mediator of angiogenesis, with binding domains of anti-angiogenic agents used for treatment of retinal diseases, such as r...

Produced waters (PW) are the largest waste associated to the production of oil and gas; they contain dissolved salts, oil (dissolved and scattered organic compounds), chemicals and salt intolerant additives to the oil well operations, suspended particles, sand and other compounds, making their treatment very tricky. In this paper, we propose the us...

Protein homodimers pose some intriguing questions about the relation between structure and stability. We approached the problem by means of a topological methodology based on protein contact networks. We correlated local interface descriptors with structure and energy global properties of the systems under analysis. We demonstrated that the graph e...

In this work, we present an extensive analysis of protein contact network topology applied to a wide data set. We extended the concept of degree distribution to graphlets, describing local connectivity patterns. We compared results to those derived from artificial networks of the same size (number of nodes), reproducing the average degree of each p...

The industrial scale production of biodiesel, the most common biofuel, requires innovative solutions to become more and more competitive with a reduced environmental impact. Microalgae are the most promising feedstock for biodiesel production since they are grown on non-arable areas and reduce the greenhouse gas emissions as well. The oil extractio...

The purpose of this paper was to develop and present a process suitable for the purification of the so-called produced waters, a by-product of crude oil extraction, by devising a treatment train aimed at industrial and agricultural water reuse. If compared to municipal wastewaters, produced waters have a very high salinity that requires specific at...

Hydrogen is an energy vector, involved in many energetic applications (fuel cells, direct use as fuel). Its traditional production relies on fossil fuels as sources and it represents a common process of the oil and gas industry. Innovative production processes may involve renewable sources (biohydrogen) to accomplish the sustainability requirements...

One major hindrance to biomass deployment, and one which only benefitted from an unbalanced development, is refining into the different fractions which have a market value. Indeed, most products obtained from oil refining owe to the level of sophistication and optimisation reached by energy-integrated fractioning (mostly, distillation) networks. Th...

From the oil plants and platforms a large amounts of wastewaters, which are considered a by-product of crude oil extraction, are produced: they are exactly known as “produced waters”, and up to now they have been treated and disposed of in deep wells on the onshore platforms or directly discharged into the sea. Extraction technology and reservoir c...

Membrane Reactors for Energy Applications and Basic Chemical Production presents a discussion of the increasing interest in membrane reactors that has emerged in recent years from both the scientific and industrial communities, in particular their usage for energy applications and basic chemical production. Part One of the text investigates membran...

Biofuels are becoming increasingly important worldwide as environmentally friendly alternatives to fossil fuels, with biofuels produced from sources that do not compete with food crops being of particular interest. This chapter discusses the advantages of using membrane technology to produce biofuels from sources such as vegetable oils, lignocellul...

Current hydrogen production processes, which depend upon the use of fossil fuels, are discussed. The means which can be used to increase efficiency, and to enable both up- and down-scaling, are considered, in particular the use of catalysts and inorganic membranes. Biomass as an alternative energy source for the production of biohydrogen through bo...